dbSNP rs10262966: POR:p.Gly2Gly (chr7-75954007-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001395413.1(POR):c.6A>G(p.Gly2Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0212 in 1,598,424 control chromosomes in the GnomAD database, including 3,076 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.080 ( 1481 hom., cov: 32)

Exomes 𝑓: 0.015 ( 1595 hom. )

Consequence

POR
NM_001395413.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts P:1B:6

Conservation

PhyloP100: 0.424

Publications

20 publications found

Variant links:

Genes affected

POR (HGNC:9208): (cytochrome p450 oxidoreductase) This gene encodes an endoplasmic reticulum membrane oxidoreductase that is essential for multiple metabolic processes, including reactions catalyzed by cytochrome P450 proteins for metabolism of steroid hormones, drugs and xenobiotics. The encoded protein has a flavin adenine dinucleotide (FAD)-binding domain and a flavodoxin-like domain which bind two cofactors, FAD and FMN, that allow it to donate electrons directly from NADPH to all microsomal P450 enzymes. Mutations in this gene cause a complex set of disorders, including apparent combined P450C17 and P450C21 deficiency, amenorrhea and disordered steroidogenesis, congenital adrenal hyperplasia and Antley-Bixler syndrome, that resemble those caused by defects in steroid metabolizing enzymes such as aromatase, 21-hydroxylase, and 17 alpha-hydroxylase. [provided by RefSeq, Aug 2020]

POR Gene-Disease associations (from GenCC):

Antley-Bixler syndrome with genital anomalies and disordered steroidogenesis
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Ambry Genetics, PanelApp Australia
congenital adrenal hyperplasia due to cytochrome P450 oxidoreductase deficiency
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
Antley-Bixler syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

POR links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 7-75954007-A-G is Benign according to our data. Variant chr7-75954007-A-G is described in ClinVar as Benign. ClinVar VariationId is 16913.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.424 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395413.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
POR	NM_001395413.1	MANE Select	c.6A>G	p.Gly2Gly	synonymous	Exon 2 of 16	NP_001382342.1	P16435
POR	NM_001382655.3		c.6A>G	p.Gly2Gly	synonymous	Exon 2 of 17	NP_001369584.2
POR	NM_001367562.3		c.6A>G	p.Gly2Gly	synonymous	Exon 3 of 17	NP_001354491.2	P16435

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
POR	ENST00000461988.6	TSL:1 MANE Select	c.6A>G	p.Gly2Gly	synonymous	Exon 2 of 16	ENSP00000419970.2	P16435
POR	ENST00000910548.1		c.6A>G	p.Gly2Gly	synonymous	Exon 2 of 16	ENSP00000580607.1
POR	ENST00000910554.1		c.6A>G	p.Gly2Gly	synonymous	Exon 2 of 16	ENSP00000580613.1

Frequencies

GnomAD3 genomes

AF:

0.0797

AC:

12131

AN:

152128

Hom.:

1468

Cov.:

show subpopulations

Gnomad AFR

AF:

0.259

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0355

Gnomad ASJ

AF:

0.0109

Gnomad EAS

AF:

0.00347

Gnomad SAS

AF:

0.0760

Gnomad FIN

AF:

0.00791

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.00328

Gnomad OTH

AF:

0.0602

GnomAD2 exomes

AF:

0.0311

AC:

7013

AN:

225548

AF XY:

0.0297

show subpopulations

Gnomad AFR exome

AF:

0.268

Gnomad AMR exome

AF:

0.0205

Gnomad ASJ exome

AF:

0.0103

Gnomad EAS exome

AF:

0.00177

Gnomad FIN exome

AF:

0.00692

Gnomad NFE exome

AF:

0.00383

Gnomad OTH exome

AF:

0.0201

GnomAD4 exome

AF:

0.0150

AC:

21765

AN:

1446178

Hom.:

1595

Cov.:

AF XY:

0.0160

AC XY:

11471

AN XY:

717982

show subpopulations

African (AFR)

AF:

0.272

AC:

9003

AN:

33118

American (AMR)

AF:

0.0226

AC:

956

AN:

42282

Ashkenazi Jewish (ASJ)

AF:

0.00929

AC:

239

AN:

25738

East Asian (EAS)

AF:

0.00433

AC:

170

AN:

39222

South Asian (SAS)

AF:

0.0699

AC:

5854

AN:

83762

European-Finnish (FIN)

AF:

0.00657

AC:

345

AN:

52544

Middle Eastern (MID)

AF:

0.0663

AC:

359

AN:

5412

European-Non Finnish (NFE)

AF:

0.00281

AC:

3101

AN:

1104246

Other (OTH)

AF:

0.0290

AC:

1738

AN:

59854

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

936

1873

2809

3746

4682

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

384

768

1152

1536

1920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0801

AC:

12198

AN:

152246

Hom.:

1481

Cov.:

AF XY:

0.0792

AC XY:

5898

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.260

AC:

10779

AN:

41494

American (AMR)

AF:

0.0355

AC:

543

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0109

AC:

AN:

3472

East Asian (EAS)

AF:

0.00347

AC:

AN:

5182

South Asian (SAS)

AF:

0.0763

AC:

368

AN:

4822

European-Finnish (FIN)

AF:

0.00791

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00328

AC:

223

AN:

68036

Other (OTH)

AF:

0.0596

AC:

126

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

486

972

1459

1945

2431

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

118

236

354

472

590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0365

Hom.:

1572

Bravo

AF:

0.0892

Asia WGS

AF:

0.0590

AC:

206

AN:

3478

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Antley-Bixler syndrome with genital anomalies and disordered steroidogenesis (2)

Congenital adrenal hyperplasia due to cytochrome P450 oxidoreductase deficiency (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

7.9

(source)

DANN

Benign

0.61

PhyloP100

0.42

PromoterAI

-0.021

Neutral

(source)

Mutation Taster

=297/3

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over